segresnet-mlx 0.2.3__tar.gz → 0.3.1__tar.gz

segresnet_mlx-0.3.1/PKG-INFO

@@ -0,0 +1,80 @@
+Metadata-Version: 2.5
+Name: segresnet-mlx
+Version: 0.3.1
+Summary: Native MLX SegResNet with NumPy sliding-window logit inference
+Project-URL: Homepage, https://huggingface.co/MedMLX/segresnet-renal-cect-mlx
+Author: Joseph Sandoval, Alfredo Sandoval Jr.
+License-Expression: Apache-2.0
+License-File: LICENSE
+License-File: THIRD_PARTY_NOTICES.md
+Classifier: Operating System :: MacOS :: MacOS X
+Requires-Python: <3.15,>=3.13
+Requires-Dist: medmlx-core==0.2.5
+Requires-Dist: nibabel<6,>=5.3
+Requires-Dist: numpy<3,>=2.0
+Provides-Extra: dev
+Requires-Dist: hypothesis<7,>=6; extra == 'dev'
+Requires-Dist: monai==1.6.1; extra == 'dev'
+Requires-Dist: pyright==1.1.414; extra == 'dev'
+Requires-Dist: pytest<10,>=8.4; extra == 'dev'
+Requires-Dist: pytorch-ignite<0.6,>=0.4.11; extra == 'dev'
+Requires-Dist: ruff<1,>=0.13; extra == 'dev'
+Requires-Dist: torch<3,>=2.6; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# segresnet-mlx
+
+Segment brain tumors, renal structures and whole-body CT anatomy with MONAI SegResNet models in native MLX.
+
+[Docs](https://github.com/MedMLX/segresnet-mlx/blob/main/docs/technical.md) · [BraTS weights](https://huggingface.co/MedMLX/segresnet-brats-mlx) · [Renal weights](https://huggingface.co/MedMLX/segresnet-renal-cect-mlx) · [MedMLX](https://github.com/MedMLX)
+
+| Input | Output |
+| :--- | :--- |
+| MRI sequences or CT volumes | Segmentation on the input grid |
+
+**Apple Silicon · Metal · Python 3.13 / 3.14** · [uv](https://docs.astral.sh/uv/)
+
+## Install
+
+```bash
+uv venv --python 3.13
+source .venv/bin/activate
+uv pip install "segresnet-mlx @ git+https://github.com/MedMLX/segresnet-mlx.git@f60afe77518f5e617145cc4ccfa8eaa59e9eeb3e"
+```
+
+This source revision validates NIfTI units, voxel values and geometry before
+inference; PyPI 0.3.0 predates those checks.
+
+## Run
+
+```python
+from segresnet_mlx.medmlx import brats
+
+result = brats(
+    t1c_path="t1c.nii.gz", t1_path="t1.nii.gz", t2_path="t2.nii.gz",
+    flair_path="flair.nii.gz", output_dir="out",
+)
+print(result["outputs"]["mask"])
+```
+
+The registered models are `segresnet-brats` and `segresnet-renal-cect`. Their `brats`
+and `renal_cect` runners select the matching bundle internally and download
+`MedMLX/segresnet-brats-mlx` or `MedMLX/segresnet-renal-cect-mlx` when `weights_path`
+is omitted. An explicit folder contains `segresnet-brats.safetensors` for BraTS or
+`segresnet-renal-cect.safetensors` for renal CECT. The renal runner takes
+`arterial_path`, `venous_path` and `excretory_path`. Keep each model's input volumes
+on one voxel grid.
+
+The standalone `run(bundle=..., weights_path=...)` interface remains available for
+explicit local checkpoints, including the whole-body CT variants. Published native
+weights are also available for [renal CECT](https://huggingface.co/MedMLX/segresnet-renal-cect-mlx)
+and [whole-body CT](https://huggingface.co/MedMLX/segresnet-wholebody-mlx).
+
+Downloaded commits are returned in `details.weights_revision`; explicit local
+weights report `null` unless the folder carries a MedMLX download revision.
+
+## License
+
+[Apache-2.0](https://github.com/MedMLX/segresnet-mlx/blob/main/LICENSE). See [third-party notices](https://github.com/MedMLX/segresnet-mlx/blob/main/THIRD_PARTY_NOTICES.md). Model weights retain their publisher terms.
+
+For research and education. Outputs require human review.

segresnet_mlx-0.3.1/README.md

@@ -0,0 +1,56 @@
+# segresnet-mlx
+
+Segment brain tumors, renal structures and whole-body CT anatomy with MONAI SegResNet models in native MLX.
+
+[Docs](https://github.com/MedMLX/segresnet-mlx/blob/main/docs/technical.md) · [BraTS weights](https://huggingface.co/MedMLX/segresnet-brats-mlx) · [Renal weights](https://huggingface.co/MedMLX/segresnet-renal-cect-mlx) · [MedMLX](https://github.com/MedMLX)
+
+| Input | Output |
+| :--- | :--- |
+| MRI sequences or CT volumes | Segmentation on the input grid |
+
+**Apple Silicon · Metal · Python 3.13 / 3.14** · [uv](https://docs.astral.sh/uv/)
+
+## Install
+
+```bash
+uv venv --python 3.13
+source .venv/bin/activate
+uv pip install "segresnet-mlx @ git+https://github.com/MedMLX/segresnet-mlx.git@f60afe77518f5e617145cc4ccfa8eaa59e9eeb3e"
+```
+
+This source revision validates NIfTI units, voxel values and geometry before
+inference; PyPI 0.3.0 predates those checks.
+
+## Run
+
+```python
+from segresnet_mlx.medmlx import brats
+
+result = brats(
+    t1c_path="t1c.nii.gz", t1_path="t1.nii.gz", t2_path="t2.nii.gz",
+    flair_path="flair.nii.gz", output_dir="out",
+)
+print(result["outputs"]["mask"])
+```
+
+The registered models are `segresnet-brats` and `segresnet-renal-cect`. Their `brats`
+and `renal_cect` runners select the matching bundle internally and download
+`MedMLX/segresnet-brats-mlx` or `MedMLX/segresnet-renal-cect-mlx` when `weights_path`
+is omitted. An explicit folder contains `segresnet-brats.safetensors` for BraTS or
+`segresnet-renal-cect.safetensors` for renal CECT. The renal runner takes
+`arterial_path`, `venous_path` and `excretory_path`. Keep each model's input volumes
+on one voxel grid.
+
+The standalone `run(bundle=..., weights_path=...)` interface remains available for
+explicit local checkpoints, including the whole-body CT variants. Published native
+weights are also available for [renal CECT](https://huggingface.co/MedMLX/segresnet-renal-cect-mlx)
+and [whole-body CT](https://huggingface.co/MedMLX/segresnet-wholebody-mlx).
+
+Downloaded commits are returned in `details.weights_revision`; explicit local
+weights report `null` unless the folder carries a MedMLX download revision.
+
+## License
+
+[Apache-2.0](https://github.com/MedMLX/segresnet-mlx/blob/main/LICENSE). See [third-party notices](https://github.com/MedMLX/segresnet-mlx/blob/main/THIRD_PARTY_NOTICES.md). Model weights retain their publisher terms.
+
+For research and education. Outputs require human review.

{segresnet_mlx-0.2.3 → segresnet_mlx-0.3.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "segresnet-mlx"
-version = "0.2.3"
+version = "0.3.1"
 description = "Native MLX SegResNet with NumPy sliding-window logit inference"
 readme = "README.md"
 requires-python = ">=3.13,<3.15"
@@ -13,22 +13,19 @@ license = "Apache-2.0"
 license-files = ["LICENSE", "THIRD_PARTY_NOTICES.md"]
 authors = [{ name = "Joseph Sandoval" }, { name = "Alfredo Sandoval Jr." }]
 dependencies = [
-  "medmlx-core==0.2.4",
+  "medmlx-core==0.2.5",
   "nibabel>=5.3,<6",
   "numpy>=2.0,<3",
 ]
 
 [project.entry-points."medmlx.models"]
-segresnet = "segresnet_mlx.medmlx:MODEL"
+segresnet-brats = "segresnet_mlx.medmlx:BRATS_MODEL"
+segresnet-renal-cect = "segresnet_mlx.medmlx:RENAL_CECT_MODEL"
 
 [project.urls]
-Homepage = "https://github.com/MedMLX/segresnet-mlx"
-Documentation = "https://github.com/MedMLX/segresnet-mlx/blob/main/docs/technical.md"
-Repository = "https://github.com/MedMLX/segresnet-mlx"
-Issues = "https://github.com/MedMLX/segresnet-mlx/issues"
+Homepage = "https://huggingface.co/MedMLX/segresnet-renal-cect-mlx"
 
 [project.optional-dependencies]
-conversion = ["torch>=2.6,<3"]
 dev = [
   "pyright==1.1.414",
   "pytorch-ignite>=0.4.11,<0.6",
@@ -64,7 +61,7 @@ select = ["E", "F", "I", "UP", "B", "SIM", "RUF"]
 
 [tool.pyright]
 include = ["scripts","src","tests"]
-extraPaths = ["src"]
+extraPaths = ["src", "scripts", "tests"]
 pythonVersion = "3.13"
 typeCheckingMode = "strict"
 enableTypeIgnoreComments = false
@@ -77,9 +74,6 @@ ban-relative-imports = "all"
 "typing.Any" = {msg = "Use a precise type and parse untyped values at the boundary."}
 "typing_extensions.Any" = {msg = "Use a precise type and parse untyped values at the boundary."}
 
-[tool.uv.sources]
-medmlx-core = { git = "https://github.com/MedMLX/medmlx.git", rev = "f98e0924f50228e2b9509474947b9672054b3217", subdirectory = "packages/core" }
-
 [tool.hatch.build.targets.sdist]
 only-include = [
   "src/segresnet_mlx",

{segresnet_mlx-0.2.3 → segresnet_mlx-0.3.1}/src/segresnet_mlx/__init__.py

@@ -16,12 +16,10 @@ if TYPE_CHECKING:
     from segresnet_mlx.predictor import predict_logits as predict_logits
     from segresnet_mlx.telemetry import WindowTelemetry as WindowTelemetry
     from segresnet_mlx.topology import SegResNetSpec as SegResNetSpec
-    from segresnet_mlx.weights import convert_checkpoint as convert_checkpoint
-    from segresnet_mlx.weights import convert_state_dict as convert_state_dict
     from segresnet_mlx.weights import load_model as load_model
     from segresnet_mlx.weights import required_shapes as required_shapes
 
-__version__ = "0.2.3"
+__version__ = "0.3.1"
 
 _EXPORTS = {
     "BUNDLE_CONFIGS": "segresnet_mlx.predictor",
@@ -30,8 +28,6 @@ _EXPORTS = {
     "SegResNetSpec": "segresnet_mlx.topology",
     "SlidingWindowConfig": "segresnet_mlx.predictor",
     "WindowTelemetry": "segresnet_mlx.telemetry",
-    "convert_checkpoint": "segresnet_mlx.weights",
-    "convert_state_dict": "segresnet_mlx.weights",
     "forward_patch": "segresnet_mlx.inference",
     "load_model": "segresnet_mlx.weights",
     "predict_logits": "segresnet_mlx.predictor",
@@ -45,8 +41,6 @@ __all__ = [
     "SegResNetSpec",
     "SlidingWindowConfig",
     "WindowTelemetry",
-    "convert_checkpoint",
-    "convert_state_dict",
     "forward_patch",
     "load_model",
     "predict_logits",
@@ -55,6 +49,7 @@ __all__ = [
 
 
 def __getattr__(name: str) -> object:
+    """Load a public export on first access and cache it in the package."""
     module = _EXPORTS.get(name)
     if module is None:
         raise AttributeError(f"module 'segresnet_mlx' has no attribute {name!r}")
@@ -64,4 +59,5 @@ def __getattr__(name: str) -> object:
 
 
 def __dir__() -> list[str]:
+    """Include lazy exports in interactive package discovery."""
     return sorted({*globals(), *_EXPORTS})

segresnet_mlx-0.3.1/src/segresnet_mlx/_nifti.py

@@ -0,0 +1,121 @@
+"""Typed protocols for the NiBabel NIfTI, header and orientation calls used here."""
+
+from __future__ import annotations
+
+from collections.abc import Sequence
+from os import PathLike
+from typing import Protocol, cast
+
+import nibabel
+import numpy as np
+from nibabel.filebasedimages import ImageFileError as ImageFileError
+
+from segresnet_mlx._arrays import Float64Array, HostArray
+
+type PathArg = str | PathLike[str]
+
+
+class ArrayBuffer(Protocol):
+    def __array__(
+        self, dtype: np.dtype[np.generic] | None = None, copy: bool | None = None
+    ) -> HostArray:
+        """Expose image data through NumPy's array conversion protocol."""
+        ...
+
+
+class NiftiHeader(Protocol):
+    def get_zooms(self) -> tuple[float, ...]:
+        """Return the voxel spacing stored in the header."""
+        ...
+
+    def set_zooms(self, zooms: Sequence[float] | Float64Array) -> None:
+        """Set voxel spacing in the header."""
+        ...
+
+    def get_xyzt_units(self) -> tuple[str, str]:
+        """Return the NIfTI spatial and temporal unit names."""
+        ...
+
+    def set_xyzt_units(self, xyz: str) -> None:
+        """Set the NIfTI spatial unit name."""
+        ...
+
+    def __getitem__(self, key: str) -> HostArray:
+        """Return a named NIfTI header field."""
+        ...
+
+    def __setitem__(self, key: str, value: int) -> None:
+        """Set an integer-valued NIfTI header field."""
+        ...
+
+
+class NiftiImage(Protocol):
+    shape: tuple[int, ...]
+    affine: Float64Array
+    dataobj: ArrayBuffer | HostArray
+    header: NiftiHeader
+
+    def __init__(self, dataobj: HostArray, affine: HostArray) -> None:
+        """Create an image from voxel data and its affine."""
+        ...
+
+    def get_data_dtype(self) -> np.dtype[np.generic]:
+        """Return the stored voxel-data dtype."""
+        ...
+
+    def get_sform(self) -> Float64Array:
+        """Return the header's sform affine."""
+        ...
+
+    def get_qform(self) -> Float64Array:
+        """Return the header's qform affine."""
+        ...
+
+    def set_sform(self, affine: Float64Array, code: int | None = None) -> None:
+        """Set the header's sform affine and optional code."""
+        ...
+
+    def set_qform(self, affine: Float64Array, code: int | None = None) -> None:
+        """Set the header's qform affine and optional code."""
+        ...
+
+
+class Orientations(Protocol):
+    def axcodes2ornt(self, axcodes: str, labels: tuple[tuple[str, str], ...]) -> Float64Array:
+        """Convert axis codes to an orientation array."""
+        ...
+
+    def ornt_transform(self, start_ornt: Float64Array, end_ornt: Float64Array) -> Float64Array:
+        """Return the transform between two orientation arrays."""
+        ...
+
+    def inv_ornt_aff(self, ornt: Float64Array, shape: Sequence[int]) -> Float64Array:
+        """Return the inverse voxel-coordinate affine for an orientation change."""
+        ...
+
+    def aff2axcodes(
+        self, aff: Float64Array, labels: tuple[tuple[str, str], ...]
+    ) -> tuple[str | None, ...]:
+        """Return axis codes implied by an affine."""
+        ...
+
+
+class Nibabel(Protocol):
+    Nifti1Image: type[NiftiImage]
+    orientations: Orientations
+
+    def load(self, filename: PathArg) -> NiftiImage:
+        """Load an image from a NIfTI path."""
+        ...
+
+    def save(self, img: NiftiImage, filename: PathArg) -> None:
+        """Write an image to a NIfTI path."""
+        ...
+
+    def io_orientation(self, affine: Float64Array) -> Float64Array:
+        """Return the input-to-output orientation implied by an affine."""
+        ...
+
+
+# Bound to the real module; this runner admits only NIfTI images.
+nib = cast(Nibabel, nibabel)

{segresnet_mlx-0.2.3 → segresnet_mlx-0.3.1}/src/segresnet_mlx/_records.py

@@ -57,8 +57,10 @@ class Details(TypedDict):
     ``requires_human_review`` is always true: outputs are research results.
     """
 
+    weights_revision: NotRequired[str | None]
     bundle: str
     arithmetic_profile: ArithmeticProfile
+    streaming: NotRequired[bool]
     labels: dict[str, str]
     labels_present: list[int]
     input_shape: list[int]

{segresnet_mlx-0.2.3 → segresnet_mlx-0.3.1}/src/segresnet_mlx/_types.py

@@ -6,20 +6,27 @@ from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
     from collections.abc import Callable, Mapping, Sequence
-    from typing import Literal, Protocol
+    from typing import Literal, Protocol, TypedDict
 
     import mlx.core as mx
     from medmlx_core.typing import MlxRuntime
+    from medmlx_core.volume_workspace import VolumeWorkspace
 
     from segresnet_mlx._arrays import Float32Array, HostArray
 
     type Array = mx.array
+
+    class WorkspaceOptions(TypedDict, total=False):
+        workspace: VolumeWorkspace
+
     type ArrayValue = bool | int | float | complex | list[ArrayValue] | tuple[ArrayValue, ...]
 
     class ArrayConstructor(Protocol):
         def __call__(
             self, value: HostArray | Array | ArrayValue, dtype: mx.Dtype | None = None
-        ) -> Array: ...
+        ) -> Array:
+            """Construct an MLX array with an optional dtype."""
+            ...
 
     class MLX(MlxRuntime, Protocol):
         all = staticmethod(mx.all)
@@ -32,7 +39,6 @@ if TYPE_CHECKING:
         load = staticmethod(mx.load)
 
         def eval(self, *args: Array | Mapping[str, Array] | Sequence[Array]) -> None: ...
-
         def save_safetensors(self, file: str, arrays: dict[str, Array]) -> None: ...
 
     class SlidingWindowInference(Protocol):
@@ -50,10 +56,15 @@ if TYPE_CHECKING:
             with_coord: bool = False,
             predictor_input: Literal["numpy"],
             preserve_window_strides: bool = False,
-        ) -> Float32Array: ...
+            workspace: VolumeWorkspace | None = None,
+        ) -> Float32Array:
+            """Blend predictor outputs from overlapping windows into host logits."""
+            ...
 
     class CoreSlidingWindow(Protocol):
         sliding_window_inference: SlidingWindowInference
 
     class Metal(Protocol):
-        def is_available(self) -> bool: ...
+        def is_available(self) -> bool:
+            """Report whether the Metal backend is available."""
+            ...